RetrogeneDB ID:

retro_ogar_2191

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873600.1:5159764..5162262(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMD1
Ensembl ID:ENSOGAG00000012201
Aliases:None
Description:proteasome (prosome, macropain) 26S subunit, non-ATPase, 1 [Source:HGNC Symbol;Acc:9554]


Retrocopy-Parental alignment summary:






>retro_ogar_2191
ATGATCATCTCAGCCGCTGGAATTATTTCTCTTCCAGATGAAGAAGAACCACAGCTTAAGGAATTTGCACTACACAAATT
GAATGCAGTTGTCAATGACTCCTGGGCAGAAATTTCTGAGTCTGTAGACAAAATAGAAGTTTTGTACGAAGATGAAGGTT
TCCAGAGTTGGCGGTTTTCAGCCTTAGTGGCATCTAAAGTATTTTATCACCTGGGGGCTTTTGAGGATCTCTGAATTATG
CTCTTGGAGCAGGTGACCTCTTCAATGTCAAAGATAACTCTGAATATGTGGAGACTATTACAGCAAAATGCATTGATCAT
TATACCAAACAGTGTGTGGAAAATGCAGATTTGCCTGAAGGAGAAAAACCAATTAACTAGAGATTGGAAGGCATTGTGAA
TAAAATGTTCCAACGATGTCTAGATGATCACAAGTATAAACAGGCTGTTGGCATCGCTTTGGAGAGACAAAGACTGGATG
TCTTCGAAAAACCCATACTGGAGTCGAATGATGTTCCAGGAATGCTAGCTTATAGCCTTAAGTTATGCATGTCTTTAATG
CAGAATAAACAGTTTCAGAATAAAGTTCTAAGAGTTCTAGTTAAAATCTACATGAACTTGGAGAAACCTAATTTCACCAA
TGTTTATCAGTGCTTAATTTTCTTAGATGATTCTCAAGCTGTGAGTGATATCTTAGAAAAACTGGTAAAGGAAGACAACC
TCCTGATGGCTTATCAGATTTGTTTTGACTTGTATGAAAGTGTTAGCCAGCAATTTTTGTCATCTGTAATTCAGAATCTT
CGAACTGTTGGCACCCCCTATTGCTTCTGTGCCTGGATCCACCAATACGGGTACTGTTCTGGAATCAGAGAAAGACAGTG
ATTAAATGGAAACAGAAGAAAAGACAGGCAGTGTACTTGTAGGAAAAACACCAGAAGCAAGTCCAGAGCCCAAGGACCAG
ACTTTGAAAATGATTAAAATTTTAAGTGGTGAAATGGCTATTGAGTTACACCTGCAGTTCTTAATACGAAACAATAACAC
AGACCTCATGATTCTAAAAAACACAAAGGAGGCAGTACGGAATTCTGTATGTCATACAGCAACTGTTATAGCAAACTCTT
TATGCACTGTGGGACTACCAGTGACCAGTTTCTTAGAGATAACTTGGAATGGTTGGCCAGAGCCACTAACTGGGCAAAAT
TTACTGCTACAGTCAGTTTGGGTGTAATTCATAAGGGTCATGAGAAGGAAGCTTTACAATTAATGGCAACATACCTTCCC
AAGGATACTTCTCCAGGATCGGCCTATCAGGAAGGTGGTGGTCTCTATGCATTGGGTCTTATTCATGCCAATCATGGTAG
TGATATCATTGACTATCTGCTTAATCAGCTTAAGAATGCCAGCAAGGATATTGTTGGGCATGGTGGCAGTTTGGGCCTTG
GTTTGGCTGCCATGGGAATCGCACATCAGAATGTGTGTGATTTGCTGAAAACAAACCTTTATCAGGATGATGCTGTCACA
GGGGAAGCAGCTGGCCTCACCCTAGGACTGGTTATGTTGGGCTCTAAAAATGCCCAGGCAATTGAGGACATGGTTGGCTA
CGCACAAGAAACTCAACATGAGAAGATTCTATGTGGTCTTGCAGTTGGCATCGCATTAGTAATGTATGGGAGGATGGAAG
AGGCTGATGCTCTCATTGAATCTCTCTGTCATGATAAGGACCCAATTCTTGGTTGGTCTAAAATGTATATTGCAGCCATG
GCCTATTGTGGCTCTGGTAACAACAAAGTTATTCGACACCTGCTACATGTTGCAGTAAGTGATGTTAATGATGATGTCAG
GAGGGCAGTAGTAGAATCACTTGGGTTTATTCTATTCACGACCCCTGAACAGTGCCCCACTGTTGTTTCTTTGTTGTCAG
AGAGCTACAACCCTCACGTGTGCTATGGAGCTGCAATGGCCTTGGGGATCTGCTGTGCTGGTACAGGAAACAAGGAAGCT
ATTAATTTGCTAGAACCCATGACAAATGACTCTGTGAACTACGTGAGGCAAGGGGCACTCATAGCTTCAGCTCTCATTAT
GATCCAGCAGACTGAAATCACTTGTCCCAAGGTGAATCAGTTCAGACAGCTATATTCCAAAGTTATCAACGATAAACATG
ATGATGTCATGGCCAAGTTTGGTGCTATCCTGGCCCAGGGCATACTGGATGCAGGTGGTCATAATGTCACAATCTCCTTA
CAGTCCAGGACTGGGCACACTCATACGCCTTCTGTGGTTGGCATTCTTGTCTTTACCCAGTTCTGGTTCTGGTTTCCTCT
TTCATACTTCCTGTCATTGGCTTATACCCCTACCTGTGTCATTGGCCTTAACAAGGACTTAAAGATGCTGAAAGTTCAGT
ATAAATCAAACTGTAAACCATCTACATTTGCATATCTTGACCCTCTGGAAGTACCAAAGGAAAAGGAAAAGGTTTCTACT
GCTGTGTTATCTATAACT

ORF - retro_ogar_2191 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.85 %
Parental protein coverage: 87.72 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMITSAAGIISLLDEEEPQLKEFALHKLNAVVNDFWAEISESVDKIEVLYEDEGFRSRQFAALVASKVFYH
MI.SAAGIISL.DEEEPQLKEFALHKLNAVVND.WAEISESVDKIEVLYEDEGF.S..F.ALVASKVFYH
RetrocopyMIISAAGIISLPDEEEPQLKEFALHKLNAVVNDSWAEISESVDKIEVLYEDEGFQSWRFSALVASKVFYH
ParentalLGAFEE-SLNYALGAGDLFNVNDNSEYVETIIAKCIDHYTKQCVENADLPEGEKKPIDQRLEGIVNKMFQ
LGAFE..SLNYALGAGDLFNV.DNSEYVETI.AKCIDHYTKQCVENADLPEGEK.PI..RLEGIVNKMFQ
RetrocopyLGAFED<SLNYALGAGDLFNVKDNSEYVETITAKCIDHYTKQCVENADLPEGEK-PIN*RLEGIVNKMFQ
ParentalRCLDDHKYKQAVGIALETRRLDVFEKTILESNDVPGMLAYSLKLCMSLMQNKQFRNKVLRVLVKIYMNLE
RCLDDHKYKQAVGIALE..RLDVFEK.ILESNDVPGMLAYSLKLCMSLMQNKQF.NKVLRVLVKIYMNLE
RetrocopyRCLDDHKYKQAVGIALERQRLDVFEKPILESNDVPGMLAYSLKLCMSLMQNKQFQNKVLRVLVKIYMNLE
ParentalKPDFINVCQCLIFLDDPQAVSDILEKLVKEDNLLMAYQICFDLYESASQQFLSSVIQNLRTVGTP-IASV
KP.F.NV.QCLIFLDD.QAVSDILEKLVKEDNLLMAYQICFDLYES.SQQFLSSVIQNLRTVGTP.IASV
RetrocopyKPNFTNVYQCLIFLDDSQAVSDILEKLVKEDNLLMAYQICFDLYESVSQQFLSSVIQNLRTVGTP>IASV
ParentalPGSTNTGTVPGSEKDSDSMETEEKTGSVLVGKTPEASPEPKDQTLKMIKILSGEMAIELHLQFLIRNNNT
PGSTNTGTV..SEKDSD.METEEKTGSVLVGKTPEASPEPKDQTLKMIKILSGEMAIELHLQFLIRNNNT
RetrocopyPGSTNTGTVLESEKDSD*METEEKTGSVLVGKTPEASPEPKDQTLKMIKILSGEMAIELHLQFLIRNNNT
ParentalDLMILKNTKDAVRNSVCHTATVIANS-FMHCGTTSDQFLRDNLEWLARATNWAKFTATASLGVIHKGHEK
DLMILKNTK.AVRNSVCHTATVIANS.FMHCGTTSDQFLRDNLEWLARATNWAKFTAT.SLGVIHKGHEK
RetrocopyDLMILKNTKEAVRNSVCHTATVIANS<FMHCGTTSDQFLRDNLEWLARATNWAKFTATVSLGVIHKGHEK
ParentalEALQLMATYLPKDTSPGSAYQEGGGLYALGLIHANHGGDIIDYLLNQLKNASNDIVRHGGSLGLGLAAMG
EALQLMATYLPKDTSPGSAYQEGGGLYALGLIHANHG.DIIDYLLNQLKNAS.DIV.HGGSLGLGLAAMG
RetrocopyEALQLMATYLPKDTSPGSAYQEGGGLYALGLIHANHGSDIIDYLLNQLKNASKDIVGHGGSLGLGLAAMG
ParentalTARQDVYDLLKTNLYQDDAVTGEAAGLALGLVMLGSKNAQAIEDMVGYAQETQHEKILRGLAVGIALVMY
.A.Q.V.DLLKTNLYQDDAVTGEAAGL.LGLVMLGSKNAQAIEDMVGYAQETQHEKIL.GLAVGIALVMY
RetrocopyIAHQNVCDLLKTNLYQDDAVTGEAAGLTLGLVMLGSKNAQAIEDMVGYAQETQHEKILCGLAVGIALVMY
ParentalGRMEEADALIESLCRDKDPILRRSGMYTVAMAYCGSGNNKAIRRLLHVAVSDVNDDVRRAAVESLGFILF
GRMEEADALIESLC.DKDPIL..S.MY..AMAYCGSGNNK.IR.LLHVAVSDVNDDVRRA.VESLGFILF
RetrocopyGRMEEADALIESLCHDKDPILGWSKMYIAAMAYCGSGNNKVIRHLLHVAVSDVNDDVRRAVVESLGFILF
ParentalRTPEQCPSVVSLLSESYNPHVRYGAAMALGICCAGTGNKEAINLLEPMTNDPVNYVRQGALIASALIMIQ
.TPEQCP.VVSLLSESYNPHV.YGAAMALGICCAGTGNKEAINLLEPMTND.VNYVRQGALIASALIMIQ
RetrocopyTTPEQCPTVVSLLSESYNPHVCYGAAMALGICCAGTGNKEAINLLEPMTNDSVNYVRQGALIASALIMIQ
ParentalQTEITCPKVNQFRQLYSKVINDKHDDVMAKFGAILAQGILDAGGHNVTISLQSRTGHTHMPSVVGVLVFT
QTEITCPKVNQFRQLYSKVINDKHDDVMAKFGAILAQGILDAGGHNVTISLQSRTGHTH.PSVVG.LVFT
RetrocopyQTEITCPKVNQFRQLYSKVINDKHDDVMAKFGAILAQGILDAGGHNVTISLQSRTGHTHTPSVVGILVFT
ParentalQFWFWFPLSHFLSLAYTPTCVIGLNKDLKMPKVQYKSNCKPSTFAYPAPLEVPKEKEKEKVSTAVLSIT
QFWFWFPLS.FLSLAYTPTCVIGLNKDLKM.KVQYKSNCKPSTFAY..PLEVP..KEKEKVSTAVLSIT
RetrocopyQFWFWFPLSYFLSLAYTPTCVIGLNKDLKMLKVQYKSNCKPSTFAYLDPLEVP--KEKEKVSTAVLSIT

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_2191 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Otolemur garnettii ENSOGAG00000012201 1 retrocopy
retro_ogar_2191 ,




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